tbuckley/cabot-search huggingface dataset:
High-Dose Docosahexaenoic Acid in Newborns Born at Less Than 29 Weeks’ Gestation and Behavior at Age 5 Years
Authors: Jacqueline F. Gould, Rachel M. Roberts, Peter J. Anderson, Maria Makrides, Thomas R. Sullivan, Robert A. Gibson, Andrew J. McPhee, Lex W. Doyle, Jana M. Bednarz, Karen P. Best, Gillian Opie, Javeed Travadi, Jeanie L. Y. Cheong, Peter G. Davis, Mary Sharp, Karen Simmer, Kenneth Tan, Scott Morris, Kei Lui, Srinivas Bolisetty, Helen Liley, Jacqueline Stack, Carmel T. Collins
Journal: JAMA Pediatrics (2023)

Children born at less than 29 weeks' gestation are at risk of behavioral difficulties. This may be due in part to the lack of transplacental supply of docosahexaenoic acid (DHA), a key fatty acid with structural and functional roles in the brain.
Rare De Novo and Inherited Genes in Familial and Nonfamilial Pediatric Attention-Deficit/Hyperactivity Disorder
Authors: Anne B. Arnett, Elizabeth Harstad, Mia O’Connell, Katheryn Hayes, Stephanie Brewster, William Barbaresi, Ryan N. Doan
Journal: JAMA Pediatrics (2023)

This case-control study examines the prevalence of rare de novo and inherited sequence variations among children and adolescents with attention-deficit/hyperactivity disorder (ADHD) and siblings and parents without ADHD.
What Health Systems Can Do Now to Improve Human Papillomavirus Vaccination
Authors: Mary Kate Kelly, Rachel A. Katzenellenbogen, Alexander G. Fiks
Journal: JAMA Pediatrics (2023)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Pediatrics HomeNew OnlineCurrent IssueFor Authors Podcast Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2024 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Pediatrics journal
ROB-ME: a tool for assessing risk of bias due to missing evidence in systematic reviews with meta-analysis
Authors: Matthew J Page, Jonathan A C Sterne, Isabelle Boutron, Asbjørn Hróbjartsson, Jamie J Kirkham, Tianjing Li, Andreas Lundh, Evan Mayo-Wilson, Joanne E McKenzie, Lesley A Stewart, Alex J Sutton, Lisa Bero, Adam G Dunn, Kerry Dwan, Roy G Elbers, Raju Kanukula, Joerg J Meerpohl, Erick H Turner, Julian P T Higgins
Journal: BMJ (2023)

Various methods are available to help users assess whether selective non-publication of studies or selective non-reporting of study results has occurred, but not its impact on a meta-analysis. This limitation of existing methods leaves users to decide their own approach for judging the risk of bias in a meta-analysis result. In this paper, Page and colleagues describe the ROB-ME (risk of bias due to missing evidence) tool, a structured approach for assessing the risk of bias that arises when entire studies, or particular results within studies, are missing from a meta-analysis because of the P value, magnitude, or direction of the study results. The tool is anticipated to help authors and users of systematic reviews identify meta-analyses at high risk of bias and interpret results appropriately.
Adipo-glial signaling mediates metabolic adaptation in peripheral nerve regeneration
Authors: Venkat Krishnan Sundaram, Vlad Schütza, Nele H. Schröter, Aline Backhaus, Annika Bilsing, Lisa Joneck, Anna Seelbach, Clara Mutschler, Jose A. Gomez-Sanchez, Erik Schäffner, Eva Ernst Sánchez, Dagmar Akkermann, Christina Paul, Nancy Schwagarus, Silvana Müller, Angela Odle, Gwen Childs, David Ewers, Theresa Kungl, Maren Sitte, Gabriela Salinas, Michael W. Sereda, Klaus-Armin Nave, Markus H. Schwab, Mario Ost, Peter Arthur-Farraj, Ruth M. Stassart, Robert Fledrich
Journal: Cell Metabolism (2023)

The peripheral nervous system harbors a remarkable potential to regenerate after acute nerve trauma. Full functional recovery, however, is rare and critically depends on peripheral nerve Schwann cells that orchestrate breakdown and resynthesis of myelin and, at the same time, support axonal regrowth. How Schwann cells meet the high metabolic demand required for nerve repair remains poorly understood. We here report that nerve injury induces adipocyte to glial signaling and identify the adipokine leptin as an upstream regulator of glial metabolic adaptation in regeneration. Signal integration by leptin receptors in Schwann cells ensures efficient peripheral nerve repair by adjusting injury-specific catabolic processes in regenerating nerves, including myelin autophagy and mitochondrial respiration. Our findings propose a model according to which acute nerve injury triggers a therapeutically targetable intercellular crosstalk that modulates glial metabolism to provide sufficient energy for successful nerve repair.
Epigenomic mapping reveals distinct B cell acute lymphoblastic leukemia chromatin architectures and regulators
Authors: Kelly R. Barnett, Robert J. Mobley, Jonathan D. Diedrich, Brennan P. Bergeron, Kashi Raj Bhattarai, Alexander C. Monovich, Shilpa Narina, Wenjian Yang, Kristine R. Crews, Christopher S. Manring, Elias Jabbour, Elisabeth Paietta, Mark R. Litzow, Steven M. Kornblau, Wendy Stock, Hiroto Inaba, Sima Jeha, Ching-Hon Pui, Charles G. Mullighan, Mary V. Relling, Shondra M. Pruett-Miller, Russell J.H. Ryan, Jun J. Yang, William E. Evans, Daniel Savic
Journal: Cell Genomics (2023)

B cell lineage acute lymphoblastic leukemia (B-ALL) is composed of diverse molecular subtypes, and while transcriptional and DNA methylation profiling has been extensively examined, the chromatin landscape is not well characterized for many subtypes. We therefore mapped chromatin accessibility using ATAC-seq in primary B-ALL cells from 156 patients spanning ten molecular subtypes and present this dataset as a resource. Differential chromatin accessibility and transcription factor (TF) footprint profiling were employed and identified B-ALL cell of origin, TF-target gene interactions enriched in B-ALL, and key TFs associated with accessible chromatin sites preferentially active in B-ALL. We further identified over 20% of accessible chromatin sites exhibiting strong subtype enrichment and candidate TFs that maintain subtype-specific chromatin architectures. Over 9,000 genetic variants were uncovered, contributing to variability in chromatin accessibility among patient samples. Our data suggest that distinct chromatin architectures are driven by diverse TFs and inherited genetic variants that promote unique gene-regulatory networks.
Advances in the understanding and management of alcohol-related liver disease
Authors: Mark Thursz, Anne Lingford-Hughes
Journal: BMJ (2023)

Alcohol-related liver disease (ALD) is a major cause of liver-related morbidity and mortality. Epidemiological trends indicate recent and predicted increases in the burden of disease. Disease progression is driven by continued alcohol exposure on a background of genetic predisposition together with environmental cofactors. Most individuals present with advanced disease despite a long history of excessive alcohol consumption and multiple missed opportunities to intervene. Increasing evidence supports the use of non-invasive tests to screen for and identify disease at earlier stages. There is a definite role for public health measures to reduce the overall burden of disease. At an individual level, however, the ability to influence subsequent disease course by modifying alcohol consumption or the underlying pathogenic mechanisms remains limited due to a comparative lack of effective, disease-modifying medical interventions. Abstinence from alcohol is the key determinant of outcome in established ALD and the cornerstone of clinical management. In those with decompensated ALD, liver transplant has a clear role. There is consensus that abstinence from alcohol for an arbitrary period should not be the sole determinant in a decision to transplant. An increasing understanding of the mechanisms by which alcohol causes liver disease in susceptible individuals offers the prospect of new therapeutic targets for disease-modifying drugs. Successful translation will require significant public and private investment in a disease area which has traditionally been underfunded when compared to its overall prevalence.
A PERK-Specific Inhibitor Blocks Metastatic Progression by Limiting Integrated Stress Response–Dependent Survival of Quiescent Cancer Cells
Authors: Veronica Calvo, Wei Zheng, Anna Adam-Artigues, Kirk A. Staschke, Xin Huang, Julie F. Cheung, Ana Rita Nobre, Sho Fujisawa, David Liu, Maria Fumagalli, David Surguladze, Michael E. Stokes, Ari Nowacek, Mark Mulvihill, Eduardo F. Farias, Julio A. Aguirre-Ghiso
Journal: Clinical Cancer Research (2023)

Abstract Purpose: The integrated stress response (ISR) kinase PERK serves as a survival factor for both proliferative and dormant cancer cells. We aim to validate PERK inhibition as a new strategy to specifically eliminate solitary disseminated cancer cells (DCC) in secondary sites that eventually reawake and originate metastasis. Experimental Design: A novel clinical-grade PERK inhibitor (HC4) was tested in mouse syngeneic and PDX models that present quiescent/dormant DCCs or growth-arrested cancer cells in micro-metastatic lesions that upregulate ISR. Results: HC4 significantly blocks metastasis, by killing quiescent/slow-cycling ISRhigh, but not proliferative ISRlow DCCs. HC4 blocked expansion of established micro-metastasis that contained ISRhigh slow-cycling cells. Single-cell gene expression profiling and imaging revealed that a significant proportion of solitary DCCs in lungs were indeed dormant and displayed an unresolved ER stress as revealed by high expression of a PERK-regulated signature. In human breast cancer metastasis biopsies, GADD34 expression (PERK-regulated gene) and quiescence were positively correlated. HC4 effectively eradicated dormant bone marrow DCCs, which usually persist after rounds of therapies. Importantly, treatment with CDK4/6 inhibitors (to force a quiescent state) followed by HC4 further reduced metastatic burden. In HNSCC and HER2+ cancers HC4 caused cell death in dormant DCCs. In HER2+ tumors, PERK inhibition caused killing by reducing HER2 activity because of sub-optimal HER2 trafficking and phosphorylation in response to EGF. Conclusions: Our data identify PERK as a unique vulnerability in quiescent or slow-cycling ISRhigh DCCs. The use of PERK inhibitors may allow targeting of pre-existing or therapy-induced growth arrested “persister” cells that escape anti-proliferative therapies.
Social Determinants of Health and Cardiologist Involvement in the Care of Adults Hospitalized for Heart Failure
Authors: David T. Zhang, Chukwuma Onyebeke, Musarrat Nahid, Lauren Balkan, Mahad Musse, Laura C. Pinheiro, Madeline R. Sterling, Raegan W. Durant, Todd M. Brown, Emily B. Levitan, Monika M. Safford, Parag Goyal
Journal: JAMA Network Open (2023)

Importance Involvement of a cardiologist in the care of adults during a hospitalization for heart failure (HF) is associated with reduced rates of in-hospital mortality and hospital readmission. However, not all patients see a cardiologist when they are hospitalized for HF. Objective To determine whether social determinants of health (SDOH) are associated with cardiologist involvement in the management of adults hospitalized for HF. Design, Setting, and Participants This retrospective cohort study used data from the Reasons for Geographic and Racial Difference in Stroke (REGARDS) cohort. Participants included adults who experienced an adjudicated hospitalization for HF between 2009 and 2017 in all 48 contiguous states in the US. Data analysis was performed from November 2022 to January 2023. Exposures A total of 9 candidate SDOH, aligned with the Healthy People 2030 conceptual model, were examined: Black race, social isolation, social network and/or caregiver availability, educational attainment less than high school, annual household income less than $35 000, living in rural area, living in a zip code with high poverty, living in a Health Professional Shortage Area, and living in a state with poor public health infrastructure. Main Outcomes and Measures The primary outcome was cardiologist involvement, defined as involvement of a cardiologist as the primary responsible clinician or as a consultant. Bivariate associations between each SDOH and cardiologist involvement were examined using Poisson regression with robust SEs. Results The study included 1000 participants (median [IQR] age, 77.8 [71.5-84.0] years; 479 women [47.9%]; 414 Black individuals [41.4%]; and 492 of 876 with low income [56.2%]) hospitalized at 549 unique US hospitals. Low annual household income (&amp;amp;lt;$35 000) was the only SDOH with a statistically significant association with cardiologist involvement (relative risk, 0.88; 95% CI, 0.82-0.95). In a multivariable analysis adjusting for age, race, sex, HF characteristics, comorbidities, and hospital characteristics, low income remained inversely associated with cardiologist involvement (relative risk, 0.89; 95% CI, 0.82-0.97). Conclusions and Relevance This cohort study found that adults with low household income were 11% less likely than adults with higher incomes to have a cardiologist involved in their care during a hospitalization for HF. These findings suggest that socioeconomic status may bias the care provided to patients hospitalized for HF.
SARS-CoV-2 and innate immunity: the good, the bad, and the “goldilocks”
Authors: Benjamin L. Sievers, Mark T. K. Cheng, Kata Csiba, Bo Meng, Ravindra K. Gupta
Journal: Cellular and Molecular Immunology (2023)

Abstract An ancient conflict between hosts and pathogens has driven the innate and adaptive arms of immunity. Knowledge about this interplay can not only help us identify biological mechanisms but also reveal pathogen vulnerabilities that can be leveraged therapeutically. The humoral response to SARS-CoV-2 infection has been the focus of intense research, and the role of the innate immune system has received significantly less attention. Here, we review current knowledge of the innate immune response to SARS-CoV-2 infection and the various means SARS-CoV-2 employs to evade innate defense systems. We also consider the role of innate immunity in SARS-CoV-2 vaccines and in the phenomenon of long COVID.
High-Sensitivity Cardiac Troponin I Enhances Preeclampsia Prediction Beyond Maternal Factors and the sFlt-1/PlGF Ratio
Authors: Lucas Bacmeister, Alina Goßling, Annette Buellesbach, Anna Birukov, Jenny E. Myers, Susan T. Thomas, Stacy Lee, Marianne S. Andersen, Jan S. Jorgensen, Anke Diemert, Sandra M. Blois, Petra C. Arck, Kurt Hecher, Florian Herse, Stefan Blankenberg, Ralf Dechend, Dirk Westermann, Tanja Zeller
Journal: Circulation (2023)

Preeclampsia shares numerous risk factors with cardiovascular diseases. Here, we aimed to assess the potential utility of high-sensitivity cardiac troponin I (hs-cTnI) values during pregnancy in predicting preeclampsia occurrence.
Transformer with convolution and graph-node co-embedding: An accurate and interpretable vision backbone for predicting gene expressions from local histopathological image
Authors: Xiao Xiao, Yan Kong, Ronghan Li, Zuoheng Wang, Hui Lu
Journal: Medical Image Analysis (2023)

Inferring gene expressions from histopathological images has long been a fascinating yet challenging task, primarily due to the substantial disparities between the two modality. Existing strategies using local or global features of histological images are suffering model complexity, GPU consumption, low interpretability, insufficient encoding of local features, and over-smooth prediction of gene expressions among neighboring sites. In this paper, we develop TCGN (Transformer with Convolution and Graph-Node co-embedding method) for gene expression estimation from H&E-stained pathological slide images. TCGN comprises a combination of convolutional layers, transformer encoders, and graph neural networks, and is the first to integrate these blocks in a general and interpretable computer vision backbone. Notably, TCGN uniquely operates with just a single spot image as input for histopathological image analysis, simplifying the process while maintaining interpretability. We validate TCGN on three publicly available spatial transcriptomic datasets. TCGN consistently exhibited the best performance (with median PCC 0.232). TCGN offers superior accuracy while keeping parameters to a minimum (just 86.241 million), and it consumes minimal memory, allowing it to run smoothly even on personal computers. Moreover, TCGN can be extended to handle bulk RNA-seq data while providing the interpretability. Enhancing the accuracy of omics information prediction from pathological images not only establishes a connection between genotype and phenotype, enabling the prediction of costly-to-measure biomarkers from affordable histopathological images, but also lays the groundwork for future multi-modal data modeling. Our results confirm that TCGN is a powerful tool for inferring gene expressions from histopathological images in precision health applications.
Cardiovascular risk in chronic hepatitis B patients treated with tenofovir disoproxil fumarate or tenofovir alafenamide
Authors: Hyeyeon Hong, Won-Mook Choi, Danbi Lee, Ju Hyun Shim, Kang Mo Kim, Young-Suk Lim, Han Chu Lee, Jonggi Choi
Journal: Clinical and Molecular Hepatology (2023)

Background/Aims: Tenofovir disoproxil fumarate (TDF) is known to have a lipid-lowering effect. This is in contrast to tenofovir alafenamide (TAF), which has a lipid-neutral effect. Therefore, concerns have been raised as to whether these differences affect long-term cardiovascular risk. Here, we aimed to evaluate the long-term risk of cardiovascular events in chronic hepatitis B (CHB) patients treated with TAF or TDF.Methods: We retrospectively analyzed 4,124 treatment-naïve CHB patients treated with TDF (n=3,186) or TAF (n=938) between 2012 and 2022. The primary outcome was a composite endpoint of major adverse cardiovascular events (MACE), including myocardial infarction, ischemic stroke, and hospitalization for unstable angina or heart failure. Serial changes in lipid profiles between two treatments were also explored.Results: The median age of the patients was 50.6 years, and 60.6% of the patients were male. At baseline, 486 (11.8%) and 637 (15.4%) of the patients had dyslipidemia and fatty liver, respectively. A total of 42 MACE occurred, with an annual incidence of 0.2%/100 person-years (PYs). At 1, 3, and 5 years, the cumulative risk of MACE was 0.4%, 0.8%, and 1.2% in patients treated with TDF, and 0.2%, 0.7%, and 0.7% in patients treated with TAF, respectively (&lt;i&gt;p&lt;/i&gt;=0.538). No significant differences in the risk of MACE were observed between TDF and TAF. A multivariable analysis found that current smoker and a history of cardiovascular events were risk factors associated with an increased risk of MACE.Conclusions: Patients treated with TAF had comparable risks of cardiovascular outcomes, defined as MACE, as patients treated with TDF.
Quality of life outcomes in patients undergoing facial gender affirming surgery: A systematic review and meta-analysis
Authors: Gavin A. Raner, Katrina M. Jaszkul, Michelle Bonapace-Potvin, Khalifa Al-Ghanim, Gabriel Bouhadana, Andrée-Anne Roy, Éric Bensimon
Journal: International Journal of Transgender Health (2023)

Facial gender-affirming surgery (FGAS), one of many transition-related surgeries (TRSs), "feminizes" the faces of transgender and gender diverse (TGD) patients undergoing transition. However, it is difficult to demonstrate the medical necessity of FGAS in terms of postoperative quality of life (QoL) outcomes due to a lack of standardized assessment tools. Thus, FGAS remains largely unsubsidized in North America.
ArcB orchestrates the quorum-sensing system to regulate type III secretion system 1 in <i>Vibrio parahaemolyticus</i>
Authors: Ce Zhang, Min Liu, Ying Wu, Xixi Li, Chen Zhang, Douglas R. Call, Ming Liu, Zhe Zhao
Journal: Gut Microbes (2023)

In many Vibrio species, virulence is regulated by quorum sensing, which is regulated by a complex, multichannel, two-component phosphorelay circuit. Through this circuit, sensor kinases transmit sensory information to the phosphotransferase LuxU via a phosphotransfer mechanism, which in turn transmits the signal to the response regulator LuxO. For Vibrio parahaemolyticus, type III secretion system 1 (T3SS1) is required for cytotoxicity, but it is unclear how quorum sensing regulates T3SS1 expression. Herein, we report that a hybrid histidine kinase, ArcB, instead of LuxU, and sensor kinase LuxQ and response regulator LuxO, collectively orchestrate T3SS1 expression in V. parahaemolyticus. Under high oxygen conditions, LuxQ can interact with ArcB directly and phosphorylates the Hpt domain of ArcB. The Hpt domain of ArcB phosphorylates the downstream response regulator LuxO instead of ArcA. LuxO then activates transcription of the T3SS1 gene cluster. Under hypoxic conditions, ArcB autophosphorylates and phosphorylates ArcA, whereas ArcA does not participate in regulating the expression of T3SS1. Our data provides evidence of an alternative regulatory path involving the quorum sensing phosphorelay and adds another layer of understanding about the environmental regulation of gene expression in V. parahaemolyticus.
A Phase I Study of the CDK4/6 Inhibitor Palbociclib in Combination with Cetuximab and Radiotherapy for Locally Advanced Head and Neck Squamous Cell Carcinoma
Authors: Nuttapong Ngamphaiboon, Poompis Pattaranutaporn, Somthawin Lukerak, Teerada Siripoon, Artit Jinawath, Lalida Arsa, Prapimporn Ch. Shantavasinkul, Naphat Taonam, Narumol Trachu, Natini Jinawath, Arpakorn Kositwattanarerk, Thiparom Sananmuang, Chuleeporn Jiarpinitnun
Journal: Clinical Cancer Research (2023)

Palbociclib, a cyclin D kinase 4 (CDK4)/6 inhibitor, has shown radiosensitizing effects in preclinical studies. There is a strong rationale for adding palbociclib to cetuximab and radiotherapy in locally advanced head and neck squamous cell carcinoma (LA-HNSCC), especially in p16-negative HNSCC.